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Then it's simpler to make changes and rebake a new version for export to Unity.
Pulling the exported model back from Unity to Blender can be like trying to un-bake the cookie to add the cinnamon to the dough.
However, if all you need to change is some coloring on materials, then like Doranos said, it would be a lot easier just to apply the edited materials to the base model in Blender itself, and you wouldn't have to rely on installing third party mods to your unity. It's honestly as easy as clicking one or two buttons.
Or you could just atlas your base model, and then paste the edited materials over the atlased files. Also really easy.
Now changing materials in blender is failry easy to do, just change the file path in the material tab and tinker around in the texture tab till the texture appear properly (basically pick between multiply or mix for the texture property, activate alpha and color rendering and then set Z-transaprancy to zero in the material tab).
Dont forget to check if the UVMap is single and properly named in the data tab (if it isnt named UVMap it wont work).
I'd recommand to find yourself a tutorial on youtube and learn to do manual atlasings too while you're at it. The automatic atlasing most of the time mess up the texture definition completely by shrinking the UVMap of your different meshes stupidly, using only a quarter of the total UVMap area to render the entire model....